1. Field of the Invention
The present invention relates generally to organ-specific proteins and polynucleotides that encode them. In particular the invention relates to diagnostic and prognostic panels, sets, and individual agents comprising reagents or probes to detect organ-specific proteins or polynucleotides and methods of identifying and using organ-specific proteins.
2. Description of the Related Art
The ability to monitor normal health and to detect the onset of disease at a very early and treatable stage is critical to diagnostic medicine. Early detection for most diseases, including diseases of the lung, cardiovascular disease, cancer, hematological disease (including most hematological cancers), inflammatory disorders, metabolic disease and neurological disease may permit treatment at an earlier stage that will produce healthier and typically more successful outcomes for the patient. Accordingly, there is a great need for more sensitive and accurate assays and methods to measure health and detect disease and monitor treatment at earlier stages.
Diagnostic assays are often incapable of identifying truly informative proteins for analyses and, to be useful, often require significant changes in protein composition in for example, blood, at the cellular level to detect the presence of disease or to define a change in health from normal. Current diagnostic assays may not detect disease until it has progressed to a stage where it is too late for effective treatment. For example, most cancers may be cured if diagnosed at the earliest stage. If cancer is diagnosed at later or advanced stages, effective treatment may be difficult or impossible and lead to reduced patient survival. In general, current diagnostic assays have severe limitations that prevent early detection and diagnosis.
In the context of blood protein diagnostics the major impediment to use in the early detection of disease is that most proteins are not disease-specific in that multiple organs synthesize them and different diseases may perturb their expression in different ways. Moreover, the specific proteins that are released in the disease state that are markers of the disease may be difficult to identify or to measure because of the enormous dynamic range of protein expression in the blood and because of the enormous protein complexity in the blood. These proteins must be distinguished from other protein markers found in the blood that are not likely to be disease markers. Other protein markers that are present in the blood that are not typically considered indicators of disease include proteins released due to: cellular damage, normal cellular turnover, stress responses (liver proteins) or other slight protein changes in the plasma. Additionally, 22 proteins constitute about 99% of the total blood protein mass. Indeed, one protein, albumin, comprises about 51% of this total blood protein mass. Most of these abundant blood proteins are not useful diagnostic markers. Useful diagnostic proteins are present in much lower abundance and typically in 1% of the remaining proteins (Lee et al., Curr Opin in Chem Bio (2006) 10:1-8). Many proteins are released into the blood following physiological changes from normal to the disease state and are likely present in plasma as low abundance proteins. Furthermore, blood proteins exhibit large differences in the concentration of the most abundant and least abundant proteins that range over many orders of magnitude. Proteins are expressed in blood across a range of about 1010 between the numbers of proteins. This means that one protein may be present at one copy in a given volume of blood, whereas another may be present at 1010 copies (Anderson and Anderson Mol and Cell Proteomics (2002) 1:845). Low abundance proteins may be hidden or dwarfed by the more prevalent high abundance proteins. Additionally, many proteins that are low abundance proteins are not indicative of disease. Distinguishing between the low abundance proteins that indicate disease from the low abundance proteins that are found in the normal cellular state is a major challenge to modern protein diagnostics. A major obstacle in diagnostic protein analysis of the blood is the numerous blood proteins and an inability by current methods to distinguish proteins from one another. Determining which blood proteins are predictive of disease at the earliest stages is very difficult at best, because the diagnostician must distinguish which low abundance protein is a marker of disease within the mass of proteins that are circulating in the blood.
Different approaches for identifying blood proteins are known in the art and have been used with varying and limited degrees of success. In particular, two-dimensional gel electrophoresis (2-DE) has been used for analysis of proteomic patterns in blood, but it is difficult to resolve large numbers of proteins such as are expressed in the average cell (up to 10,000 proteins). Moreover, 2-DE is incapable of identifying low abundance proteins without enrichment techniques. Another method known in the art for blood protein diagnostics is capillary isoelectric focusing electrophoresis (CGE) although, the lack of reproducibility of protein patterns limits its use (Corthals, G. L., et al. Electrophoresis, (1997), 18:317, Lopez, M. F., and W. F. Patton, Electrophoresis, (1997), 18:338). Consequently, protein pattern analysis using techniques such as 2-DE, CGE and other similar techniques cannot generally be used for the analysis of blood proteins due to the inability to detect very low abundance proteins, irreproducible gel patterns, and the inability to quantify or identify individual spots (e.g., proteins). Further, the ability to extend these techniques to reproducible, consistent, easy to use and accurate high throughput diagnostic assays has been extremely limited. Thus, current assays that detect proteins do not provide the accuracy to use levels of blood (or other biological fluid or tissue) proteins, polypeptides or nucleic acids to monitor health and disease.
It is evident that a new diagnostic strategy is needed to distinguish between the many proteins that are found in the blood that reflect the normal health of a mammal and the organ-specific proteins that reflect a state of disease.
For the foregoing reasons, there is a need in the art to provide diagnostic and prognostic assays, nucleic acid and protein panels and arrays as well as methods to monitor health and diagnose disease. The present invention provides compositions, methods and assays that fulfill these and other needs.